Which is the most reliable snp validation technique?
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Hi everyone,
I would be interested in your opinion about most widely used metrics to assess genetic diversity, particularly when considering markers specific features.
Expected heterozygosity, allelic richness and privates alleles are common in microsatellites-based studies for example. It seems He/Ho and nucleotide diversity are widely used for high-density SNP data, haplotype diversity providing additional information if GBS is used.
However when working with medium density dataset (~100 SNP) without any knowledge about the genome and no sequence data, I feel like classical measures like He or polymorphism rates might be tricky to compare, for example if I want to compare genetic diversity between two geographic regions. I am afraid to be lacking of statistical power, especially when number of individuals in a location is also low;
Would you have any idea/personally recommand a particular approach to this end ? Could you recommand any paper about study of genetic diversity of SNP aside from HTS ?
I thank you very much for your question and wish you a very nice day :)
@chetan2222.
I would be interested in your opinion about most widely used metrics to assess genetic diversity, particularly when considering markers specific features.
Expected heterozygosity, allelic richness and privates alleles are common in microsatellites-based studies for example. It seems He/Ho and nucleotide diversity are widely used for high-density SNP data, haplotype diversity providing additional information if GBS is used.
However when working with medium density dataset (~100 SNP) without any knowledge about the genome and no sequence data, I feel like classical measures like He or polymorphism rates might be tricky to compare, for example if I want to compare genetic diversity between two geographic regions. I am afraid to be lacking of statistical power, especially when number of individuals in a location is also low;
Would you have any idea/personally recommand a particular approach to this end ? Could you recommand any paper about study of genetic diversity of SNP aside from HTS ?
I thank you very much for your question and wish you a very nice day :)
@chetan2222.
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